Merge pull request #2013 from chaitanyakasaraneni/add-samplesheetparser-testdata

Add test samplesheets for samplesheetparser modules

Author: matthdsm

README.md

@@ -500,6 +500,8 @@ The earth sciences folder contain subfolders for different data formats encounte
     - bcl:
       - flowcell.tar.gz: bcl data generated on a MiSeq sequencer. Contains only data for the first tile.
       - flowcell_samplesheet.csv: SampleSheet for data on flowcell
+      - flowcell_samplesheet.v1.csv: Illumina SampleSheet in IEM V1 (bcl2fastq) format — dual-index, 5 samples across 2 projects and 2 lanes. For samplesheet validation/parsing tests only; not intended to be run against `flowcell.tar.gz`.
+      - flowcell_samplesheet.v2.csv: Illumina SampleSheet in BCLConvert V2 format — dual-index, 5 samples across 2 projects and 2 lanes. For samplesheet validation/parsing tests only; not intended to be run against `flowcell.tar.gz`.
     - cram:
       - test.paired*end.sorted: Mapped, and sorted reads based on `test*{1,2}` (normal)
       - test.paired*end.markduplicates.sorted: Mapped, sorted, and duplicate marked reads based on `test*{1,2}` (normal)

data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.v1.csv

@@ -0,0 +1,27 @@
+[Header]
+IEMFileVersion,5
+Experiment Name,240115_A01234_0042_AHJLG7DRXX
+Date,2024-01-15
+Workflow,GenerateFASTQ
+Application,FASTQ Only
+Instrument Type,NovaSeq 6000
+Assay,TruSeq DNA PCR-Free
+Index Adapters,TruSeq DNA UD Indexes (96 Indexes)
+Chemistry,Amplicon
+
+[Reads]
+151
+151
+
+[Settings]
+ReverseComplement,0
+Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+
+[Data]
+Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+1,Sample1,SampleOne,,A01,UDP0001,CAAGACAGAT,UDP0001,ACTATAGCCT,ProjectAlpha,WGS_batch1
+1,Sample2,SampleTwo,,B01,UDP0002,TGAACCTGAT,UDP0002,TGATACGTCC,ProjectAlpha,WGS_batch1
+1,Sample3,SampleThree,,C01,UDP0003,GCACAACGTT,UDP0003,CATCTCACAG,ProjectAlpha,WGS_batch1
+2,Sample4,SampleFour,,D01,UDP0004,ATCGCCTGTT,UDP0004,GACTAGCATG,ProjectBeta,WGS_batch2
+2,Sample5,SampleFive,,E01,UDP0005,CTTGTAGCAA,UDP0005,TGCGTCAGCC,ProjectBeta,WGS_batch2

data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.v2.csv

@@ -0,0 +1,24 @@
+[Header]
+FileFormatVersion,2
+RunName,240115_LH00336_0025_A227HGJLT3
+InstrumentPlatform,NovaSeqXSeries
+
+[Reads]
+Read1Cycles,151
+Read2Cycles,151
+Index1Cycles,10
+Index2Cycles,10
+
+[BCLConvert_Settings]
+SoftwareVersion,3.9.3
+AdapterRead1,CTGTCTCTTATACACATCT
+AdapterRead2,CTGTCTCTTATACACATCT
+OverrideCycles,Y151;I10;I10;Y151
+
+[BCLConvert_Data]
+Lane,Sample_ID,Sample_Name,Index,Index2,Sample_Project
+1,Sample1,SampleOne,ATTACTCGAT,TATAGCCTGT,ProjectAlpha
+1,Sample2,SampleTwo,TCCGGAGACC,ATAGAGGCAC,ProjectAlpha
+1,Sample3,SampleThree,TAGGCATGCA,CCTATCCTAG,ProjectAlpha
+2,Sample4,SampleFour,CTCTCTACGC,GGCTCTGAGA,ProjectBeta
+2,Sample5,SampleFive,CGGAGCCTAA,AGGCGAAGAG,ProjectBeta